MiMeDB: Showing metabocard for Pyocyanine (MMDBc0001315)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-14 19:34:49 UTC

Update Date

2024-04-30 19:33:49 UTC

Metabolite ID

MMDBc0001315

Metabolite Identification

Common Name

Pyocyanine

Description

pyocyanine belongs to the class of organic compounds known as phenazines and derivatives. These are polycyclic aromatic compounds containing a phenazine moiety, which is a linear tricyclic system that consists of a two benzene rings joined by a pyrazine ring. pyocyanine is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review a significant number of articles have been published on pyocyanine.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI


  Mrv0541 05031421462D          

 16 18  0  0  0  0            999 V2000
    2.8579    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    2.4750    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  2  0  0  0  0
  5  2  1  0  0  0  0
  6  3  1  0  0  0  0
  7  4  1  0  0  0  0
  8  4  2  0  0  0  0
  9  5  2  0  0  0  0
 10  6  2  0  0  0  0
 10  9  1  0  0  0  0
 11  7  2  0  0  0  0
 12  8  1  0  0  0  0
 13 11  1  0  0  0  0
 13 12  1  0  0  0  0
 14  9  1  0  0  0  0
 14 13  2  0  0  0  0
 15  1  1  0  0  0  0
 15 10  1  0  0  0  0
 15 11  1  0  0  0  0
 16 12  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0001315

> <DATABASE_NAME>
MIME

> <SMILES>
CN1C2=CC=CC=C2N=C2C(=O)C=CC=C12

> <INCHI_IDENTIFIER>
InChI=1S/C13H10N2O/c1-15-10-6-3-2-5-9(10)14-13-11(15)7-4-8-12(13)16/h2-8H,1H3

> <INCHI_KEY>
YNCMLFHHXWETLD-UHFFFAOYSA-N

> <FORMULA>
C13H10N2O

> <MOLECULAR_WEIGHT>
210.2313

> <EXACT_MASS>
210.079312952

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
22.189724117142777

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5-methyl-1,5-dihydrophenazin-1-one

> <ALOGPS_LOGP>
1.90

> <JCHEM_LOGP>
2.4985149463333327

> <ALOGPS_LOGS>
-2.72

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
0.7791664245141825

> <JCHEM_POLAR_SURFACE_AREA>
32.67

> <JCHEM_REFRACTIVITY>
68.05930000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.00e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pyocyanine

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 03-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-MAY-14         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   16  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1   15                                                            
CONECT    2    3    5                                                       
CONECT    3    2    6                                                       
CONECT    4    7    8                                                       
CONECT    5    2    9                                                       
CONECT    6    3   10                                                       
CONECT    7    4   11                                                       
CONECT    8    4   12                                                       
CONECT    9    5   10   14                                                  
CONECT   10    6    9   15                                                  
CONECT   11    7   13   15                                                  
CONECT   12    8   13   16                                                  
CONECT   13   11   12   14                                                  
CONECT   14    9   13                                                       
CONECT   15    1   10   11                                                  
CONECT   16   12                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   36    0
END

COMPND    HMDB0256934
HETATM    1  C1  UNL     1      -0.266   2.316   0.206  1.00  0.00           C  
HETATM    2  N1  UNL     1      -0.055   0.908   0.085  1.00  0.00           N  
HETATM    3  C2  UNL     1       1.171   0.348   0.039  1.00  0.00           C  
HETATM    4  C3  UNL     1       2.324   1.090   0.114  1.00  0.00           C  
HETATM    5  C4  UNL     1       3.571   0.501   0.067  1.00  0.00           C  
HETATM    6  C5  UNL     1       3.707  -0.879  -0.058  1.00  0.00           C  
HETATM    7  C6  UNL     1       2.571  -1.655  -0.136  1.00  0.00           C  
HETATM    8  O1  UNL     1       2.727  -2.900  -0.249  1.00  0.00           O  
HETATM    9  C7  UNL     1       1.308  -1.102  -0.092  1.00  0.00           C  
HETATM   10  N2  UNL     1       0.181  -1.826  -0.163  1.00  0.00           N  
HETATM   11  C8  UNL     1      -1.041  -1.211  -0.112  1.00  0.00           C  
HETATM   12  C9  UNL     1      -2.190  -1.981  -0.185  1.00  0.00           C  
HETATM   13  C10 UNL     1      -3.468  -1.469  -0.141  1.00  0.00           C  
HETATM   14  C11 UNL     1      -3.594  -0.104  -0.017  1.00  0.00           C  
HETATM   15  C12 UNL     1      -2.452   0.698   0.059  1.00  0.00           C  
HETATM   16  C13 UNL     1      -1.188   0.145   0.011  1.00  0.00           C  
HETATM   17  H1  UNL     1      -0.953   2.620  -0.650  1.00  0.00           H  
HETATM   18  H2  UNL     1      -0.872   2.570   1.131  1.00  0.00           H  
HETATM   19  H3  UNL     1       0.604   2.966   0.140  1.00  0.00           H  
HETATM   20  H4  UNL     1       2.296   2.158   0.214  1.00  0.00           H  
HETATM   21  H5  UNL     1       4.477   1.089   0.126  1.00  0.00           H  
HETATM   22  H6  UNL     1       4.699  -1.297  -0.091  1.00  0.00           H  
HETATM   23  H7  UNL     1      -2.069  -3.051  -0.282  1.00  0.00           H  
HETATM   24  H8  UNL     1      -4.353  -2.091  -0.200  1.00  0.00           H  
HETATM   25  H9  UNL     1      -4.552   0.393   0.026  1.00  0.00           H  
HETATM   26  H10 UNL     1      -2.585   1.763   0.158  1.00  0.00           H  
CONECT    1    2   17   18   19
CONECT    2    3   16
CONECT    3    4    4    9
CONECT    4    5   20
CONECT    5    6    6   21
CONECT    6    7   22
CONECT    7    8    8    9
CONECT    9   10   10
CONECT   10   11
CONECT   11   12   12   16
CONECT   12   13   23
CONECT   13   14   14   24
CONECT   14   15   25
CONECT   15   16   16   26
END

Synonyms

Value	Source
Pyocyanin	ChEBI
Pyocyanine	MeSH

Molecular Formula

C₁₃H₁₀N₂O

Average Mass

210.2313

Monoisotopic Mass

210.079312952

IUPAC Name

5-methyl-1,5-dihydrophenazin-1-one

Traditional Name

pyocyanine

CAS Registry Number

Not Available

SMILES

CN1C2=CC=CC=C2N=C2C(=O)C=CC=C12

InChI Identifier

InChI=1S/C13H10N2O/c1-15-10-6-3-2-5-9(10)14-13-11(15)7-4-8-12(13)16/h2-8H,1H3

InChI Key

YNCMLFHHXWETLD-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as phenazines and derivatives. These are polycyclic aromatic compounds containing a phenazine moiety, which is a linear tricyclic system that consists of a two benzene rings joined by a pyrazine ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazanaphthalenes

Sub Class

Benzodiazines

Direct Parent

Phenazines and derivatives

Alternative Parents

Substituents

Phenazine
Benzenoid
Pyrazine
Heteroaromatic compound
Vinylogous amide
Azacycle
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.4 g/L	ALOGPS
logP	1.9	ALOGPS
logP	2.5	ChemAxon
logS	-2.7	ALOGPS
pKa (Strongest Basic)	0.78	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	32.67 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	68.06 m³·mol⁻¹	ChemAxon
Polarizability	22.19 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-01q9-2930000000-9ddb4c750d7f1d4078b3	2021-09-23	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-014i-0900000000-dba6c02ff82ca7f5d74a	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-03di-0190000000-a185b869dd0a45456173	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0090000000-51125ab4de88d0ea93fb	2021-09-20	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Firmicutes	1	Human feces; Human	Metabolic reconstruction
Bacteria	Proteobacteria	1	Human

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

HMDB0256934

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

6558

KEGG Compound ID

Not Available

BioCyc ID

CPD-12847

BiGG ID

Not Available

Wikipedia Link

Pyocyanin

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

8653

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for Pyocyanine (MMDBc0001315)

MOL for #<Metabolite:0x00007fece1863cf8>

3D MOL for #<Metabolite:0x00007fece1863cf8>

3D SDF for #<Metabolite:0x00007fece1863cf8>

3D-SDF for #<Metabolite:0x00007fece1863cf8>

PDB for #<Metabolite:0x00007fece1863cf8>

3D PDB for #<Metabolite:0x00007fece1863cf8>

SMILES for #<Metabolite:0x00007fece1863cf8>

INCHI for #<Metabolite:0x00007fece1863cf8>

Structure for #<Metabolite:0x00007fece1863cf8>

3D Structure for #<Metabolite:0x00007fece1863cf8>